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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatctttccagtaaaatccatgtgtgccagatcttcctttcagtgctattatgtcaaagttatatcacggcttaattttattccgttctgttggtttgactaattaattttccatattaattatcagttcatttctttacatgaattcatcctacttatggattgagcccttggctcatatcag

Basic information

species Zea mays
transcript GRMZM2G102349_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102349_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g63010.2 (Oryza sativa), 5'ss of exon 3
TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatctttccagtaaaatccatgtgtgccagatcttcctttcagtgctattatgtcaaagttatatcacggcttaattttattccgttctgttggtttgactaattaattttccatattaattatcagttcatttctttacatgaattcatcctacttatggattgagcccttggctcatatcag
||||||||||||||| ||||||||||||||  ||||||||||| |||| || ||||||||  |||||| ||| ||||| ||||| ||||| ||||||||||||||  |||  |   |    ||  ||     |||  | |   |  | |||| ||   ||    ||  ||  |   |||  ||   |  |  ||||| |  |  |                                                                                    
TCACATGTATGAAACATTTGGCTGGTGGAGGAGAGCTGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCACCTCTTAATCATGGAAgtacgtctctagctctttctgtc--tgcacatcagtgcatttatata-tgctgtttcttcctgttttgatgtccttttagattatgttag--ctgttagcatatc------------------------------------------------------------------------------------

upper sequence: GRMZM2G102349_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os04g57320.1 (Oryza sativa), 5'ss of exon 4
TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatctttccagtaaaatccatgtgtgccagatcttcctttcagtgctattatgtcaaagttatatcacggcttaattttattccgttctgttggtttgactaattaattttccatattaattatcagttcatttctttacatgaattcatcctacttatggattgagcccttggctcatatcag
||||||||||||||||||||||||||||||  |||| |||||| |||| || ||||||||  |||||| ||| ||||| ||||| ||||| |||||||||||| |  |||  |   |    ||  ||     |||  | | | |  | |||| ||   ||    ||| ||  |   |||  ||   |     ||||| |  |  |                                                                                    
TCACATGTATGAAACCTTTGGCTGGTGGAGGAGAGCCGATTATATAAAGGTGCACTTTGCTGAGAGCTGGAATGAGTTCCATCACCTCTTAATCATGGAAgtatgtctctagctctttctgtc--tgcacatcagtgcattcatata-tgctgtttcttcctgtttagatgtccttttagattatgttaa--ctgttagcatatc------------------------------------------------------------------------------------

upper sequence: GRMZM2G102349_T01 (Zea mays), 5'ss of exon 4
lower sequence: Vv00s0399g00060.t01 (Vitis vinifera), 5'ss of exon 4
TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatctttccagtaaaatccatgtgtgccagatcttcctttcagtgctattatgtcaaagttatatcacggcttaattttattccgttctgttggtttgactaattaattttccatattaattatcagttcatttctttacatgaattcatcctacttatggattgagcccttggctcatatcag
 ||||||||||| |  ||||||||||||||| | || |||||||| || || || |||||| |||||| ||| ||  | ||||||||  | |||||||||||||   |||| |   ||| ||   | |   |   ||| |  |||||  |||      |     || | |     |||  ||| |||  | | |||    |||   || |                                                                               
GCACATGTATGAGAGTTTTGGCTGGTGGAGAAGGGCGGATTATCTGAAGGTGCATTTTGCGGAGAGCTGGAATGAAATGCATCATCTGCTTATCATGGAAgtactgttcttact--taagatt--ttttaccttaatcatattttcaa-gcttcctcat-----ttgttttt---ctttgtttcattatggtgtgtcatcttggagaagtttc----------------------------------------------------------------------------

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|149101185|gb|EE187296.2|EE187296
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|148980796|gb|EE027352.2|EE027352
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|211275870|gb|FL438426.1|FL438426
EST:     TCACTTTGCGCAGAAGCTTGAACGAGTTTCATCATTTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TCACTTTGCGCAG-AGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|60345087|gb|DN212060.1|DN212060
EST:     CAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: CAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|91048932|gb|EB159350.1|EB159350
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|78545030|gb|DV622528.1|DV622528
EST:     CGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: CGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|91871244|gb|EB401317.1|EB401317
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|89755436|gb|DY685853.1|DY685853
EST:     TTCATCATCTCTTGATCATGGAA                         GAATTGGGGGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|94476406|gb|EB705364.1|EB705364
EST:     TTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|148999937|gb|EE036995.2|EE036995
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|67013464|gb|CO442213.1|CO442213
EST:     TCACTTTGCGCAGCA-CTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TCACTTTGCGCAG-AGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|76018164|gb|DT945334.1|DT945334
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|149080867|gb|EE169947.2|EE169947
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|60357246|gb|DN224219.1|DN224219
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|89759812|gb|DY688510.1|DY688510
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|148952083|gb|EC897874.2|EC897874
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
EST: gi|78116561|gb|DV534948.1|DV534948
EST:     TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAA                         GAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG
genomic: TTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATG

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 9

TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATGGCGTTTTTTTACTACTTCATGACTGTTGCGATGTACATGTTGAGCCCAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 45

TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATGGCGTTTTTTTACTACTTCATGACTGTTGCGATGTACATGTTGAGCCCAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36

TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATGGCGTTTTTTTACTACTTCATGACTGTTGCGATGTACATGTTGAGCCCAC


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 154

TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatct ... ctcatatcagGAATTGGGTGGCAACGCTATATGGATTGATTGTTTCCTTGCTCGATTTATGGCGTTTTTTTACTACTTCATGACTGTTGCGATGTACATGTTGAGCCCAC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCACATGTATGAAACCTTTGGCTGGTGGAGACGAGCTGATTATCTAAAAGTTCACTTTGCGCAGAGCTTGAACGAGTTTCATCATCTCTTGATCATGGAAgtacgcatctttccagtaaaatccatgtgtgccagatcttcctttcagtgctattatgtcaaagttatatcacggcttaattttattccgttctgttggtttgactaattaattttccatattaattatcagttcatttctttacatgaattcatcctacttatggattgagcccttggctcatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA